proteobench package

ProteoBench.

Subpackages

• proteobench.datapoint package
  • DatapointBase
    • DatapointBase.generate_datapoint()
    • DatapointBase.generate_id()
    • DatapointBase.get_metrics()
  • QuantDatapointHYE
    • QuantDatapointHYE.id
    • QuantDatapointHYE.software_name
    • QuantDatapointHYE.software_version
    • QuantDatapointHYE.search_engine
    • QuantDatapointHYE.search_engine_version
    • QuantDatapointHYE.ident_fdr_psm
    • QuantDatapointHYE.ident_fdr_peptide
    • QuantDatapointHYE.ident_fdr_protein
    • QuantDatapointHYE.enable_match_between_runs
    • QuantDatapointHYE.precursor_mass_tolerance
    • QuantDatapointHYE.fragment_mass_tolerance
    • QuantDatapointHYE.enzyme
    • QuantDatapointHYE.allowed_miscleavages
    • QuantDatapointHYE.min_peptide_length
    • QuantDatapointHYE.max_peptide_length
    • QuantDatapointHYE.is_temporary
    • QuantDatapointHYE.intermediate_hash
    • QuantDatapointHYE.results
    • QuantDatapointHYE.median_abs_epsilon_global
    • QuantDatapointHYE.mean_abs_epsilon_global
    • QuantDatapointHYE.median_abs_epsilon_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_eq_species
    • QuantDatapointHYE.median_abs_epsilon_precision_global
    • QuantDatapointHYE.mean_abs_epsilon_precision_global
    • QuantDatapointHYE.median_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.nr_prec
    • QuantDatapointHYE.comments
    • QuantDatapointHYE.proteobench_version
    • QuantDatapointHYE.allowed_miscleavages
    • QuantDatapointHYE.comments
    • QuantDatapointHYE.enable_match_between_runs
    • QuantDatapointHYE.enzyme
    • QuantDatapointHYE.fragment_mass_tolerance
    • QuantDatapointHYE.generate_datapoint()
    • QuantDatapointHYE.generate_id()
    • QuantDatapointHYE.get_count_metrics()
    • QuantDatapointHYE.get_cv_metrics()
    • QuantDatapointHYE.get_epsilon_metrics()
    • QuantDatapointHYE.get_metrics()
    • QuantDatapointHYE.get_metrics_old()
    • QuantDatapointHYE.get_precision_metrics()
    • QuantDatapointHYE.get_roc_metrics()
    • QuantDatapointHYE.id
    • QuantDatapointHYE.ident_fdr_peptide
    • QuantDatapointHYE.ident_fdr_protein
    • QuantDatapointHYE.ident_fdr_psm
    • QuantDatapointHYE.intermediate_hash
    • QuantDatapointHYE.is_temporary
    • QuantDatapointHYE.max_peptide_length
    • QuantDatapointHYE.mean_abs_epsilon_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_global
    • QuantDatapointHYE.mean_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_precision_global
    • QuantDatapointHYE.median_abs_epsilon_eq_species
    • QuantDatapointHYE.median_abs_epsilon_global
    • QuantDatapointHYE.median_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.median_abs_epsilon_precision_global
    • QuantDatapointHYE.min_peptide_length
    • QuantDatapointHYE.nr_prec
    • QuantDatapointHYE.precursor_mass_tolerance
    • QuantDatapointHYE.proteobench_version
    • QuantDatapointHYE.results
    • QuantDatapointHYE.search_engine
    • QuantDatapointHYE.search_engine_version
    • QuantDatapointHYE.software_name
    • QuantDatapointHYE.software_version
  • Submodules
    • proteobench.datapoint.datapoint_base module
      • DatapointBase
    • proteobench.datapoint.denovo_datapoint module
      • DenovoDatapoint
      • calculate_prc()
      • collapse_aa_scores()
      • get_prc_curve()
    • proteobench.datapoint.quant_datapoint module
      • QuantDatapointHYE
      • compute_roc_auc()
      • compute_roc_auc_directional()
      • filter_df_numquant_epsilon()
      • filter_df_numquant_nr_prec()
• proteobench.github namespace
  • Submodules
    • proteobench.github.gh module
      • GithubProteobotRepo
• proteobench.io package
  • Subpackages
    • proteobench.io.params package
      • ProteoBenchParameters
      • Submodules
    • proteobench.io.parsing package
      • Submodules
• proteobench.modules package
  • Subpackages
    • proteobench.modules.denovo package
      • Submodules
    • proteobench.modules.quant package
      • Submodules
    • proteobench.modules.rescoring package
      • Submodules
  • Submodules
    • proteobench.modules.constants module
• proteobench.plotting package
  • LFQHYEPlotGenerator
    • LFQHYEPlotGenerator.generate_in_depth_plots()
    • LFQHYEPlotGenerator.get_in_depth_plot_descriptions()
    • LFQHYEPlotGenerator.get_in_depth_plot_layout()
    • LFQHYEPlotGenerator.plot_main_metric()
  • PlotGeneratorBase
    • PlotGeneratorBase.generate_in_depth_plots()
    • PlotGeneratorBase.get_in_depth_plot_descriptions()
    • PlotGeneratorBase.get_in_depth_plot_layout()
    • PlotGeneratorBase.plot_main_metric()
  • Submodules
    • proteobench.plotting.plot_denovo module
      • DeNovoPlotGenerator
      • flatten_results_column()
    • proteobench.plotting.plot_generator_base module
      • PlotGeneratorBase
    • proteobench.plotting.plot_generator_lfq_HYE module
      • LFQHYEPlotGenerator
• proteobench.score package
  • QuantScoresHYE
    • QuantScoresHYE.compute_condition_stats()
    • QuantScoresHYE.compute_epsilon()
    • QuantScoresHYE.convert_replicate_to_raw()
    • QuantScoresHYE.generate_intermediate()
  • ScoreBase
    • ScoreBase.generate_intermediate()
  • Subpackages
    • proteobench.score.denovo package
      • Submodules
    • proteobench.score.quant namespace
      • Submodules
  • Submodules
    • proteobench.score.score_base module
      • ScoreBase
• proteobench.utils package
  • Submodules
    • proteobench.utils.get_plots module
    • proteobench.utils.server_io module
      • dataset_folder_exists()
      • download_file()
      • get_merged_json()
      • get_raw_data()
      • make_submission()
    • proteobench.utils.submission module
      • get_submission_dict()

Submodules

• proteobench.exceptions module
  • ConvertStandardFormatError
  • DatapointAppendError
  • DatapointGenerationError
  • DatasetAlreadyExistsOnServerError
  • IntermediateFormatGenerationError
  • ParseError
  • ParseSettingsError
  • PlotError
  • ProteoBenchError
  • ProteobenchError
  • QuantificationError
  • ValidationError